Clinical Metagenomic Next-Generation Sequencing for Pathogen Detection

被引：846

作者：

Gu, Wei ^{[1
]}

Miller, Steve ^{[1
]}

Chiu, Charles Y. ^{[1
,2
]}

机构：

[1] Univ Calif San Francisco, Dept Lab Med, San Francisco, CA 94107 USA

[2] Univ Calif San Francisco, Div Infect Dis, Dept Med, San Francisco, CA 94107 USA

来源：

ANNUAL REVIEW OF PATHOLOGY: MECHANISMS OF DISEASE, VOL 14 | 2019年 / 14卷

关键词：

clinical diagnostics; metagenomics; next-generation sequencing; pathogen detection; infectious disease; nanopore sequencing; REAL-TIME; DIAGNOSIS; RNA; DNA; IDENTIFICATION; INFECTION; STANDARDS; SAMPLES; ORIGIN; VALIDATION;

D O I：

10.1146/annurev-pathmechdis-012418-012751

中图分类号：

R36 [病理学];

学科分类号：

100104 ;

摘要：

Nearly all infectious agents contain DNA or RNA genomes, making sequencing an attractive approach for pathogen detection. The cost of high-throughput or next-generation sequencing has been reduced by several orders of magnitude since its advent in 2004, and it has emerged as an enabling technological platform for the detection and taxonomic characterization of microorganisms in clinical samples from patients. This review focuses on the application of untargeted metagenomic next-generation sequencing to the clinical diagnosis of infectious diseases, particularly in areas in which conventional diagnostic approaches have limitations. The review covers (a) next-generation sequencing technologies and common platforms, (b) next-generation sequencing assay workflows in the clinical microbiology laboratory, (c) bioinformatics analysis of metagenomic next-generation sequencing data, (d) validation and use of metagenomic next-generation sequencing for diagnosing infectious diseases, and (e) significant case reports and studies in this area. Next-generation sequencing is a new technology that has the promise to enhance our ability to diagnose, interrogate, and track infectious diseases.

引用

页码：319 / 338

页数：20

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